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- PDB-8uhj: anti-Phosphohistidine Fab hSC44.ck.20.N32F -

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Basic information

Entry
Database: PDB / ID: 8uhj
Titleanti-Phosphohistidine Fab hSC44.ck.20.N32F
Components
  • hSC44.ck.20.N32F Fab light chain
  • hSC44h.ck.20.N32F Fab heavy chain
KeywordsIMMUNE SYSTEM / ANTI-PHOSPHOHISTIDINE ANTIBODY POST-TRANSLATIONAL MODIFICATION ANTIBODY HUMANIZATION
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsKalagiri, R. / Stanfield, R.L. / Hunter, T. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA242443 United States
CitationJournal: Biorxiv / Year: 2024
Title: Using phage display for rational engineering of a higher affinity humanized 3' phosphohistidine-specific antibody.
Authors: Martyn, G.D. / Kalagiri, R. / Veggiani, G. / Stanfield, R.L. / Choudhuri, I. / Sala, M. / Meisenhelder, J. / Chen, C. / Biswas, A. / Levy, R.M. / Lyumkis, D. / Wilson, I.A. / Hunter, T. / Sidhu, S.S.
History
DepositionOct 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: hSC44h.ck.20.N32F Fab heavy chain
L: hSC44.ck.20.N32F Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0469
Polymers47,5102
Non-polymers5367
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-54 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.471, 73.253, 96.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody hSC44h.ck.20.N32F Fab heavy chain


Mass: 23597.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fab heavy chain / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#2: Antibody hSC44.ck.20.N32F Fab light chain


Mass: 23912.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fab light chain / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris, pH 8.5, 0.2M lithium sulfate, 40% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.94→48.05 Å / Num. obs: 36687 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 27.39 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.067 / Rrim(I) all: 0.193 / Rsym value: 0.18 / Χ2: 1.093 / Net I/σ(I): 12.6
Reflection shellResolution: 1.94→1.98 Å / Redundancy: 7.6 % / Rmerge(I) obs: 2.38 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1806 / CC1/2: 0.374 / CC star: 0.738 / Rpim(I) all: 0.884 / Rrim(I) all: 2.54 / Rsym value: 2.38 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→48.05 Å / SU ML: 0.2636 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2473 1846 5.04 %
Rwork0.2175 34775 -
obs0.219 36621 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.43 Å2
Refinement stepCycle: LAST / Resolution: 1.94→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 31 118 3421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00273378
X-RAY DIFFRACTIONf_angle_d0.65724588
X-RAY DIFFRACTIONf_chiral_restr0.045516
X-RAY DIFFRACTIONf_plane_restr0.0048581
X-RAY DIFFRACTIONf_dihedral_angle_d13.54031194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-20.35151380.31152460X-RAY DIFFRACTION93.42
2-2.050.33171330.29152648X-RAY DIFFRACTION100
2.05-2.120.34291340.27622659X-RAY DIFFRACTION99.96
2.12-2.20.25981390.24722671X-RAY DIFFRACTION100
2.2-2.280.33111400.24912662X-RAY DIFFRACTION100
2.28-2.390.31041290.24182649X-RAY DIFFRACTION100
2.39-2.510.29981320.25052679X-RAY DIFFRACTION100
2.51-2.670.26031620.24122669X-RAY DIFFRACTION100
2.67-2.880.29891670.25282648X-RAY DIFFRACTION100
2.88-3.170.2691390.23542700X-RAY DIFFRACTION99.89
3.17-3.630.23951540.2032695X-RAY DIFFRACTION100
3.63-4.570.17821570.1662741X-RAY DIFFRACTION99.9
4.57-48.050.1831220.18312894X-RAY DIFFRACTION99.9

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